713 Lecture 2

The species problem

What is a bacterial species?

• Phenotypic similarity• Similarity in DNA sequence• Similarity in genome content

– Entire genome?– Core genome?

• Frequency of recombination

Mayr’s biological species concept

• Species were once conceived by taxonomists as groups of similar organisms

• Mayr introduced the need for biological cohesive forces maintaining the group– Recombination– Selection (natural and sexual)

Importance of the BSC

• Emphasized importance of reproductive isolation

• Focused studies of underlying mechanisms (not physical but evolutionary)

• Identified distinct species within phenotypically similar groups and lumped other groups

Does the BSC work for prokaryotes?

Strategies for speciating bacteria

1. Phenotypic similarity• FAME• Biolog/API

2. DNA-DNA hybridization

3. 16s ribosomal DNA sequence similarity

Bacterial classification strategies

• Problem: lacks fundamental principle

• 1st, cluster on basis of phenotype

• 2nd, find DNA:DNA hybridization values that fit phenotype clusters– New method: average nucleotide identity, or

ANI

• 3rd, find value for 16s sequence similarity that fits DNA:DNA hybridization value

Does the BSC work for prokaryotes?

Prokaryotic population genetics

• Population sizes (N) are usually huge, so genetic drift is typically ineffective

• Mutation rates are typically low, but N is large, so genetic variation is abundant

• Recombination rates are VERY LOW, relative to typical diploid sexual species (and even relative to infrequent outcrossing species, like plants) – How frequent is bacterial recombination?

More challenges to fit prokaryotes into the eukaryotic BSC

• Promiscuity of homologous recombination (not just within species)

• Constraints on exchange– Ecology– Vectors– % DNA similarity:1-3% animals, 25% bacteria– Size of DNA fragment

• HGT = horizontal gene transfer = nonhomologous recombination

The alternative: the ecotype (Cohan)

The ecotype is a lesser unit than a species that highlights niche specificity and local adaptationMotivation: apparently low recombination rates

undermine the BSC

Origin of ecotypes

• New mutation generates new opportunity or selective advantage

• Little/no recombination, so new subpopulation diverges without constraint

• problem: a clean theoretical definition but realistic to find?

Periodic selection

• Simply: the purging of genetic diversity within a population by the selective sweep of a beneficial mutation

Do ecotypes become species? (it depends on recombination)

Are these ecotypes the beginning of speciation?

Poltak and Cooper

The relationship between ecotype and genotype

• Do genotypes coincide with ecotypes?

• Periodic selection should purge diversity within the lineage

• Ecotypes should form single, coalescent sequence clusters

• What about dispersal?

MLST

Sequence conserved loci (genes)Each nucleotide substitution defines a new alleleChanges at each locus occur independently and randomlySimilarity = identity by descentShared changes = recombination

MLST, eBURST ecotype?

“Why does MLST work so well?”• How long do ecotypes last?

• Can MLST divine species barriers?

What’s the best model to explain how your favorite bacterial species arose?